Data Scenario and Model Hypothesis

Standard fit report for fits of hierSCAL to DERPA data.

Data Scenario: 1956_allFleets

Model Hypothesis: baseModel

Species: Dover, English, Rock

Stocks: HSHG, QCS, WCVI

Final phase convergence diagnostics

Max Gradient: 0.0448653

Objective Function value: -1286.0359798

Time to fit model: 19.5005167

Full complex

Spawning Biomass

Spawning biomass (red line), catch (grey bars), and scaled biomass indices (coloured points), for all stocks and species. Indices are scaled by the fleet catchability, then by the ratio of spawning biomass to vulnerable biomass.

Figure 1: Spawning biomass (red line), catch (grey bars), and scaled biomass indices (coloured points), for all stocks and species. Indices are scaled by the fleet catchability, then by the ratio of spawning biomass to vulnerable biomass.

Fits to indices

Standardised vulnerable biomass (coloured lines) and the scaled and standardised biomass indices they are fitting to (coloured points), for all stocks and species.

Figure 2: Standardised vulnerable biomass (coloured lines) and the scaled and standardised biomass indices they are fitting to (coloured points), for all stocks and species.

Standardised residuals for model fits to biomass indices (coloured points) and a loess smoother with a 20% confidence interval (coloured lines and grey regions), for all fleets, stocks, and species.

Figure 3: Standardised residuals for model fits to biomass indices (coloured points) and a loess smoother with a 20% confidence interval (coloured lines and grey regions), for all fleets, stocks, and species.

Recruitment

Age-1 recruitments for all species and stocks. Equilibrium unfished recruitment $R_0$ is indicated by the horizontal dashed line.

Figure 4: Age-1 recruitments for all species and stocks. Equilibrium unfished recruitment \(R_0\) is indicated by the horizontal dashed line.

Deviations from expected recruitment for all species and stocks.

Figure 5: Deviations from expected recruitment for all species and stocks.

Stock-recruit curves (solid lines) and modeled recruitments (grey points), gridded over species (columns) and stocks (rows).

Figure 6: Stock-recruit curves (solid lines) and modeled recruitments (grey points), gridded over species (columns) and stocks (rows).

Time-varying catchability

Fishing mortality

Estimates of fishing mortality from each fleet (coloured points and lines), gridded over species (columns) and stocks (rows). Fishing mortality rates are found using an iterative Newton-Rhapson solver conditioned on the observed catch.

Figure 7: Estimates of fishing mortality from each fleet (coloured points and lines), gridded over species (columns) and stocks (rows). Fishing mortality rates are found using an iterative Newton-Rhapson solver conditioned on the observed catch.

Modeled removals (blue points) using estimated fishing mortality compared to observed catches (open circles), gridded over species (columns) and stocks (rows).

Figure 8: Modeled removals (blue points) using estimated fishing mortality compared to observed catches (open circles), gridded over species (columns) and stocks (rows).

Growth (Probability of Length-at-age)

Probability curves of length-at-age for males (blue) and females (red). Curves show the probability of each length within an age group, and opacity of the lines increases with age.

Figure 9: Probability curves of length-at-age for males (blue) and females (red). Curves show the probability of each length within an age group, and opacity of the lines increases with age.

Selectivity

Selectivity-at-length for each fleet, gridded over species (columns) and stocks (rows).

Figure 10: Selectivity-at-length for each fleet, gridded over species (columns) and stocks (rows).

Selectivity-at-age for each fleet, for females only, gridded over species (columns) and stocks (rows).

Figure 11: Selectivity-at-age for each fleet, for females only, gridded over species (columns) and stocks (rows).

Reference Points

Yield Curves

Equilibrium yield curves as a function of fishing mortality rates, assuming all fishing mortality comes from the modern trawl fleet.

Figure 12: Equilibrium yield curves as a function of fishing mortality rates, assuming all fishing mortality comes from the modern trawl fleet.

Goldilocks Plots

Re-read Hilborn 2018 for the goldilocks plot

Table

Table 1: Biological reference points for each stock and species.
Species Stock B0 R0 M_m M_f h Bmsy Fmsy Umsy MSY SSB_T D_T Dmsy_T
Dover HSHG 17.46 3.14 0.13 0.08 0.77 6.04 0.19 0.17 0.64 6.01 0.34 1
Dover QCS 5.94 1.21 0.14 0.09 0.77 1.97 0.17 0.15 0.23 1.69 0.28 0.86
Dover WCVI 15.15 4.59 0.17 0.11 0.77 5 0.21 0.19 0.71 3.98 0.26 0.8
English HSHG 9.98 4.78 0.16 0.12 0.79 3.42 0.37 0.32 0.69 6.01 0.6 1.76
English QCS 0.57 0.32 0.19 0.14 0.8 0.19 0.34 0.29 0.04 0.38 0.67 2
English WCVI 0.9 0.47 0.18 0.13 0.8 0.3 0.34 0.29 0.07 0.37 0.41 1.23
Rock HSHG 16.34 5.54 0.25 0.17 0.75 5.75 0.27 0.23 0.83 8.46 0.52 1.47
Rock QCS 5.55 1.57 0.23 0.15 0.76 1.89 0.24 0.21 0.3 1.61 0.29 0.85
Rock WCVI 1.72 0.38 0.2 0.14 0.74 0.63 0.26 0.23 0.08 0.7 0.41 1.11

Recruitment correlations

Standardised recruitment deviations. Blue indicates a positive deviation, red indicates a negative deviation, and the area of each circle is proportional to the size of the deviation.

Figure 13: Standardised recruitment deviations. Blue indicates a positive deviation, red indicates a negative deviation, and the area of each circle is proportional to the size of the deviation.

Individual species

UNDER CONSTRUCTION

Compositional data

Growth

Optimisation performance

Phase fit table

Table 2: Optimisation performance of hierSCAL for each phase.
phase objFun maxGrad nPar convCode convMsg time mcmcTime
1 1005.5757 0.0000539 33 0 relative convergence (4) 0.4234000 NA
2 -285.7490 0.0018599 42 0 relative convergence (4) 1.0169833 NA
3 -288.1209 0.0048975 44 0 relative convergence (4) 0.9178667 NA
4 -565.3093 0.0021900 404 0 relative convergence (4) 1.0744667 NA
5 -571.1965 0.0424105 413 0 relative convergence (4) 1.7255167 NA
6 -571.6236 0.0451117 422 0 relative convergence (4) 2.3463500 NA
7 -640.5282 0.0301879 425 0 relative convergence (4) 2.8796667 NA
8 -750.0643 0.0630976 431 0 relative convergence (4) 2.4864167 NA
9 -1264.0039 0.0573926 454 0 relative convergence (4) 2.4073167 NA
10 -1264.0039 0.0008141 454 0 relative convergence (4) 1.5402167 NA
11 -1286.0360 0.0448653 475 0 relative convergence (4) 2.6823167 NA
RE NA NA NA NA NA NA NA